I have a tree farm underground and I have discovered that saplings regularly disappear from it. I googled a bit on it and it seems there is a bug in 1.0 where saplings sometimes disappear for some reason.

So if anyone notices that saplings are gone, that is a bug.

If anyone knows any way to get around it, feel free to tell me.

Edit:
Doing some testing with bonemeal it seems like the saplings have a chance to disappear in the actual moment of growth. Many times when I right clicked a sapling with bonemeal when it should have grown it instead simply disappeared.

yes this happened to me many times while I was creating my treelined path for the castle ... i could see no reason for it as I was not inside or in dark or a restricted space, quite often I would leave and come back to find almost 50% gone